I would love to see some engineering drawings or section cuts of the cylinder heads.  "Pre-Chamber" makes me think of IDI diesels and the Riccardo style combustion chamber, which obviously was fairly effective and millions were built.  I am not sure if this engine uses a similar setup, or something completely different.

Yeah, it is a common misconception.  There are software packages that can take the scanned data and create a non-parametric 3D CAD models of fairly simple geometries, but they are very expensive, require a very clean scan, and still only produce a model that is difficult to manipulate any further.  The industry is getting better, but there is still a long way to go.  I have been playing with 3D scanners for about the past 10 years at various jobs.  Normally get a phone call once or twice a year from a sales rep for Keyence, Faro, or someone else promising me that their latest gadget is the greatest thing since sliced bread, I will have 3D CAD models in 2 minutes, blah, blah, blah.  I invite them in for a demo, and typically I set a compressor housing off a turbo on the table and ask them to generate a model of the involute volume.  Of course they can't because the scanners require line-of-sight and I would have to section the housing along multiple planes, take multiple scans of each section, stitch the scans together, and then import the scan geometry into CAD and use it as a guide to build a proper parametric CAD model.  If the rep gets snotty, I ask them to scan the DT-466 display model we have in the lobby.  "Well you have to disassemble it first..." In the end, the 6 figure price tag just doesn't justify the results.  They are good for resolving simple external geometries, mounting faces, and hole patterns. Complex castings and assemblies, the technology just isn't there yet. 

Scanners do not create a 3D model.  Typically they just create point clouds that can be used to generate a 3D CAD model, which can still be a ton of work.  That said, I would love to have an accurate 3D CAD model of an FE block, and an MEL, and a Y-Block....

I have used an Innovate setup a couple of times.  Works good, though I wish the O2 sensors had a longer life span.  Weld in bungs can be purchased from any of the big box online retailers (Summit, Speedway, Jegs, etc.)  Or, get the tap from McMaster-Carr and make your own.

They are invaluable for dialing a motor in.  To many detergents and additives in today's gasoline to accurately read plugs. 

Jay,
   You are spot on.  I have actually seen E85 with percentages as low as 50%.  The "85" is just a maximum standard, no real minimum % standard exists as long as the fuel meets a few other performance requirements.

And yes, E85 loves boost.  I got to play around with it in a turbocharged 1100 cc twin cylinder snowmobile engine about a decade ago.  Spent many hours on the development dyno seeing what the engine could take and what the fuel system would support.  We stopped at 330 hp when the crank came out the bottom of the engine....  Ended up dialing it back to 280 hp and dropped it into a chassis.  It would about pull your arms out of your shoulders when the boost hit. 

I don't buy exhaust kits any more.  My stuff and what I work on is rarely stock, and therefore there is no sense since I will be cutting it up and modifying it to fit anyways.  I typically buy a bunch of stainless 180 deg. mandrel U or J bends and cut the bends I need and weld it back together.  Just finished a complete exhaust system for a '60 T-Bird.  FPA headers, and all stainless 3 inch tube after that.  The only "catalog" headers I have purchased in the past 10 years came from FPA.  I did purchase a 3.5" Banks kit for my '85 F350, still had to modify the down pipe coming off the turbo, but the rest fit pretty good.

If the bumpsides are anything like the '76 Dentside F250 (last of the 390's) I did a few years ago, it was very easy.  Mostly straight pipe and just a couple of bends.  Brought the drivers side over to the passenger side and ran both pipes parrallel down the passenger side.  Used a pair of "truck" can style mufflers and exited the pipes right behind the rear wheel.  It looked stockish, but definitely did not sound or preform like a stock system. 

Sounds like a Stage II Buick V6.  Snatch it up, find a mid 80's Camaro, drop it in and embarrass the heck out of all the 350 fanboys.  Stage II's have been known to make ridiculous (1500+ HP) power with the right turbo and 2+ HP/ci in NA form is also quite doable.

Can you use a standard resistor of say 35 or 40 ohms to bypass the sender and see if the gauge reacts appropriately?  Re-reading your original post definitely makes it sound like a ground issue, but using a known resistor may help point you in the right direction.